DOCSLIB.ORG

Complete Genome Sequence of Parvibaculum Lavamentivorans Type Strain (DS-1T)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Complete Genome Sequence of Parvibaculum Lavamentivorans Type Strain (DS-1T) Erschienen in: Standards in Genomic Sciences ; 5 (2011), 3. - S. 298-310 Standards in Genomic Sciences (2011) 5:298-310 DOI:10.4056/sigs.2215005 Complete genome sequence of Parvibaculum T lavamentivorans type strain (DS-1 ) David Schleheck1*, Michael Weiss1, Sam Pitluck2, David Bruce3, Miriam L. Land4, Shunsheng Han3, Elizabeth Saunders3, Roxanne Tapia3, Chris Detter3, Thomas Brettin4, James Han2, Tanja Woyke2, Lynne Goodwin3, Len Pennacchio2, Matt Nolan2, Alasdair M. Cook1, Staffan Kjelleberg5, Torsten Thomas5 1 Department of Biological Sciences and Research School Chemical Biology, University of Konstanz, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia *Corresponding author: [email protected] Keywords: Parvibaculum lavamentivorans DS-1, aerobic, Gram-negative, Rhodobiaceae, sur- factant biodegradation Parvibaculum lavamentivorans DS-1T is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Al- phaproteobacteria. Strain DS-1T is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that cata- lyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first com- pleted genome sequence of the genus Parvibaculum, and the first genome sequence of a rep- resentative of the family Rhodobiaceae. Introduction Parvibaculum lavamentivorans strain DS-1T P. lavamentivorans DS-1T is therefore an example (DSM13023 = NCIMB13966) was isolated for its of a first tier member of a two-step process that ability to degrade linear alkylbenzenesulfonate mineralizes environmentally important surfac- (LAS), a major laundry surfactant with a world- tants. wide use of 2.5 million tons per annum [1]. Strain Other representatives of the novel genus Parviba- DS-1T was difficult to isolate, is difficult to culti- culum have been recently isolated. Parvibaculum vate, and represents a novel genus in the Alpha- sp. strain JP-57 was isolated from seawater [6] proteobacteria [2,3]. Strain DS-1 catalyzes not only and is also difficult to cultivate [3]. Parvibaculum the degradation of LAS, but also of 16 other com- indicum sp. nov. was also isolated from seawater, mercially important anionic and non-ionic surfac- via an enrichment culture that degraded polycyc- tants (hence the species name lavamentivorans = lic aromatic hydrocarbons (PAH) and crude oil [7]. consuming [chemicals] used for washing [3]). The Another Parvibaculum sp. strain was isolated from initial degradation as catalyzed by strain DS-1T a PAH-degrading enrichment culture, using river involves the activation and shortening of the alkyl- sediment as inoculum [8]. Parvibaculum species chain of the surfactant molecules, and the excre- were also reported in a study on marine alkane- tion of short-chain degradation intermediates. degrading bacteria [9]. Parvibaculum species are These intermediates are then completely utilized frequently detected by cultivation-independent by other bacteria in the community [4,5]. methods, predominantly in habitats or settings The Genomic Standards Consortium Konstanzer Online-Publikations-System (KOPS) URL: http://nbn-resolving.de/urn:nbn:de:bsz:352-177182 Schleheck et al. with hydrocarbon degradation. These include a succinate, or alkanes, alkanols and alkanoates (C8 - bacterial community on marine rocks polluted C16); no sugars tested were utilized [3]. with diesel oil [10], a bacterial community from To allow for growth in liquid culture with most of diesel-contaminated soil [11], a petroleum- the 16 different surfactants at high concentrations degrading bacterial community from seawater (e.g. for LAS, >1 mM; see [3].), the culture fluid [12], an oil-degrading cyanobacterial community needs to be supplemented with a solid surface, e.g. [13] and biofilm communities in pipes of a district polyester fleece or glass fibers [2,3]. The addition- heating system [14]. Parvibaculum species have al solid surface is believed to support biofilm for- also been detected in denitrifying, linear- mation, especially in the early growth phase when nonylphenol (NP) degrading enrichment cultures the surfactant concentration is high, and the or- from NP-polluted river sediment [15] and in ganism grows as single, suspended cells (non- groundwater that had been contaminated by li- motile) during the later growth phase. Growth near alkyl benzenes (LABs; non-sulfonated LAS] with a non-membrane toxic substrate (e.g. ace- [16]. Additionally, Parvibaculum species were tate) is independent of a solid surface, and consti- detected in biofilms that degraded polychlori- tutes suspended, single cells (motile). We presume nated biphenyls (PCBs) using pristine soil as in- that the biofilm formation by strain DS-1T is a pro- oculum [17], and in a PAH-degrading bacterial tective response to the exposure to membrane- community from deep-sea sediment of the West solubilizing agents (cf. [30]). Pacific [18]. Finally, Parvibaculum species were Based on the 16S rRNA gene sequence, strain DS1T detected in an autotrophic Fe(II)-oxidizing, ni- was described as the novel genus Parvibaculum, trate-reducing enrichment culture [19], as well as which was originally placed in the family Phyllo- in Tunisian geothermal springs [20]. The wide- bacteriaceae within the order Rhizobiales of Al- spread occurrence of Parvibaculum species in ha- phaproteobacteria [3,31]. The nearest well- bitats or settings related to hydrocarbon degrada- described organism to strain DS-1T is Afifella ma- tion implies an important function and role of rina (formerly Rhodobium marinum) (92% 16S these organisms in environmental biodegradation, rRNA gene sequence identity), a photosynthetic despite their attribute as being difficult to culti- purple, non-sulfur bacterium. The genus Rhodo- vate in a laboratory. bium was later re-classified as a member of the Here we present a summary classification and a novel family Rhodobiaceae [26,32], together with set of features for P. lavamentivorans DS-1T, to- two novel genera of other photosynthetic purple gether with the description of a complete genome non-sulfur bacteria (Afifella and Roseospirillum), sequence and annotation. The genome sequencing as well as with two novel genera of heterotrophic and analysis was part of the Microbial Genome aerobic bacteria, represented by the red- Program of the DOE Joint Genome Institute. pigmented Anderseniella baltica (gen. nov., sp. nov.) [33,34] and non-pigmented Tepidamorphus Classification and features gemmatus (gen. nov., sp. nov.) [35,36]. A phyloge- P. lavamentivorans DS-1T is a Gram-negative, non- netic tree (Figure 2) was constructed with the 16S pigmented, very small (approx. 1.0 × 0.2 µm), rRNA gene sequence of P. lavamentivorans DS-1T slightly curved rod-shaped bacterium that can be and that of (i) other isolated Parvibaculum strains, motile by means of a polar flagellum (Figure 1, (ii) representatives of other genera within the Table 1). Strain DS-1T grows very slowly on com- family Rhodobiaceae, (iii) representatives of the plex medium (e.g. on LB- or peptone-agar plates) genera in the family Phyllobacteriaceae, as well as, and forms pinpoint colonies only after more than (iv) representatives of other families within the two weeks of incubation. The organism can be order Rhizobiales. The phylogenetic tree shows quickly overgrown by other organisms. Larger now the placement of Parvibaculum species within colonies are obtained when the complex medium the family Rhodobiaceae, and that the Parvibacu- is supplemented with a surfactant, e.g. Tween 20 lum sequences clustered as a distinct evolutionary (see DSM-medium 884 [29]) or LAS [3]. When lineage within this family (Figure 2). This classifi- cultivated in liquid culture with mineral-salts me- cation of Parvibaculum has been adopted in the dium, strain DS-1T grows within one week with Ribosomal Database Project (RDP) and SILVA the single carbon sources acetate, ethanol, or rRNA Database Project, but not in the GreenGenes database. The family Rhodobiaceae has also not http://standardsingenomics.org 299 Parvibaculum lavamentivorans type strain (DS-1T) been included in the NCBI-taxonomy, IMG- phosphatidyl glycerol, diphosphatidyl glycerol, taxonomy, and GOLD databases. phosphatidyl ethanolamine, phosphatidyl choline, Currently, 360 genome sequences of members of and two, unidentified aminolipids; the presence of the order Rhizobiales of Alphaproteobacteria have the two additional aminolipids appears to be dis- been made available (GOLD database; August tinctive of the organism [3]. The G+C content of 2011), and within the family Phyllobacteriaceae the DNA was determined to be 64% [3], which there are 21 genome sequences available corresponds well to the G+C content observed for (Chelativorans sp. BNC1, Hoeflea phototrophica the complete genome sequence (see below). DFL-43, and 18 Mesorhizobium strains). No ge- nome sequences currently exist for a representa- Genome sequencing information tive of the novel family Rhodobiaceae, except
Load more

Recommended publications
  • Sphingopyxis Italica, Sp. Nov., Isolated from Roman Catacombs 1 2
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE IJSEM Papers in Press. Published December 21, 2012 as doi:10.1099/ijs.0.046573-0 provided by Digital.CSIC 1 Sphingopyxis italica, sp. nov., isolated from Roman catacombs 2 3 Cynthia Alias-Villegasª, Valme Jurado*ª, Leonila Laiz, Cesareo Saiz-Jimenez 4 5 Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, 6 Apartado 1052, 41080 Sevilla, Spain 7 8 * Corresponding author: 9 Valme Jurado 10 Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC 11 Apartado 1052, 41080 Sevilla, Spain 12 Tel. +34 95 462 4711, Fax +34 95 462 4002 13 E-mail: [email protected] 14 15 ª These authors contributed equally to this work. 16 17 Keywords: Sphingopyxis italica, Roman catacombs, rRNA, sequence 18 19 The sequence of the 16S rRNA gene from strain SC13E-S71T can be accessed 20 at Genbank, accession number HE648058. 21 22 A Gram-negative, aerobic, motile, rod-shaped bacterium, strain SC13E- 23 S71T, was isolated from tuff, the volcanic rock where was excavated the 24 Roman Catacombs of Saint Callixtus in Rome, Italy. Analysis of 16S 25 rRNA gene sequences revealed that strain SC13E-S71T belongs to the 26 genus Sphingopyxis, and that it shows the greatest sequence similarity 27 with Sphingopyxis chilensis DSMZ 14889T (98.72%), Sphingopyxis 28 taejonensis DSMZ 15583T (98.65%), Sphingopyxis ginsengisoli LMG 29 23390T (98.16%), Sphingopyxis panaciterrae KCTC12580T (98.09%), 30 Sphingopyxis alaskensis DSM 13593T (98.09%), Sphingopyxis 31 witflariensis DSM 14551T (98.09%), Sphingopyxis bauzanensis DSM 32 22271T (98.02%), Sphingopyxis granuli KCTC12209T (97.73%), 33 Sphingopyxis macrogoltabida KACC 10927T (97.49%), Sphingopyxis 34 ummariensis DSM 24316T (97.37%) and Sphingopyxis panaciterrulae T 35 KCTC 22112 (97.09%).
    [Show full text]
  • A Noval Investigation of Microbiome from Vermicomposting Liquid Produced by Thai Earthworm, Perionyx Sp
    International Journal of Agricultural Technology 2021Vol. 17(4):1363-1372 Available online http://www.ijat-aatsea.com ISSN 2630-0192 (Online) A novel investigation of microbiome from vermicomposting liquid produced by Thai earthworm, Perionyx sp. 1 Kraisittipanit, R.1,2, Tancho, A.2,3, Aumtong, S.3 and Charerntantanakul, W.1* 1Program of Biotechnology, Faculty of Science, Maejo University, Chiang Mai, Thailand; 2Natural Farming Research and Development Center, Maejo University, Chiang Mai, Thailand; 3Faculty of Agricultural Production, Maejo University, Thailand. Kraisittipanit, R., Tancho, A., Aumtong, S. and Charerntantanakul, W. (2021). A noval investigation of microbiome from vermicomposting liquid produced by Thai earthworm, Perionyx sp. 1. International Journal of Agricultural Technology 17(4):1363-1372. Abstract The whole microbiota structure in vermicomposting liquid derived from Thai earthworm, Perionyx sp. 1 was estimated. It showed high richness microbial species and belongs to 127 species, separated in 3 fungal phyla (Ascomycota, Basidiomycota, Mucoromycota), 1 Actinomycetes and 16 bacterial phyla (Acidobacteria, Armatimonadetes, Bacteroidetes, Balneolaeota, Candidatus, Chloroflexi, Deinococcus, Fibrobacteres, Firmicutes, Gemmatimonadates, Ignavibacteriae, Nitrospirae, Planctomycetes, Proteobacteria, Tenericutes and Verrucomicrobia). The OTUs data analysis revealed the highest taxonomic abundant ratio in bacteria and fungi belong to Proteobacteria (70.20 %) and Ascomycota (5.96 %). The result confirmed that Perionyx sp. 1
    [Show full text]
  • Colwellia and Marinobacter Metapangenomes Reveal Species
    bioRxiv preprint doi: https://doi.org/10.1101/2020.09.28.317438; this version posted September 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Colwellia and Marinobacter metapangenomes reveal species-specific responses to oil 2 and dispersant exposure in deepsea microbial communities 3 4 Tito David Peña-Montenegro1,2,3, Sara Kleindienst4, Andrew E. Allen5,6, A. Murat 5 Eren7,8, John P. McCrow5, Juan David Sánchez-Calderón3, Jonathan Arnold2,9, Samantha 6 B. Joye1,* 7 8 Running title: Metapangenomes reveal species-specific responses 9 10 1 Department of Marine Sciences, University of Georgia, 325 Sanford Dr., Athens, 11 Georgia 30602-3636, USA 12 13 2 Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, Georgia 14 30602-7229, USA 15 16 3 Grupo de Investigación en Gestión Ecológica y Agroindustrial (GEA), Programa de 17 Microbiología, Facultad de Ciencias Exactas y Naturales, Universidad Libre, Seccional 18 Barranquilla, Colombia 19 20 4 Microbial Ecology, Center for Applied Geosciences, University of Tübingen, 21 Schnarrenbergstrasse 94-96, 72076 Tübingen, Germany 22 23 5 Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, 24 USA 25 26 6 Integrative Oceanography Division, Scripps Institution of Oceanography, UC San 27 Diego, La Jolla, CA 92037, USA 28 29 7 Department of Medicine, University of Chicago, Chicago, IL, USA 30 31 8 Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA 32 33 9Department of Genetics, University of Georgia, 120 Green St., Athens, Georgia 30602- 34 7223, USA 35 36 *Correspondence: Samantha B.
    [Show full text]
  • Metaproteomics Characterization of the Alphaproteobacteria
    Avian Pathology ISSN: 0307-9457 (Print) 1465-3338 (Online) Journal homepage: https://www.tandfonline.com/loi/cavp20 Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) José Francisco Lima-Barbero, Sandra Díaz-Sanchez, Olivier Sparagano, Robert D. Finn, José de la Fuente & Margarita Villar To cite this article: José Francisco Lima-Barbero, Sandra Díaz-Sanchez, Olivier Sparagano, Robert D. Finn, José de la Fuente & Margarita Villar (2019) Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssusgallinae (De Geer, 1778), Avian Pathology, 48:sup1, S52-S59, DOI: 10.1080/03079457.2019.1635679 To link to this article: https://doi.org/10.1080/03079457.2019.1635679 © 2019 The Author(s). Published by Informa View supplementary material UK Limited, trading as Taylor & Francis Group Accepted author version posted online: 03 Submit your article to this journal Jul 2019. Published online: 02 Aug 2019. Article views: 694 View related articles View Crossmark data Citing articles: 3 View citing articles Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=cavp20 AVIAN PATHOLOGY 2019, VOL. 48, NO. S1, S52–S59 https://doi.org/10.1080/03079457.2019.1635679 ORIGINAL ARTICLE Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) José Francisco Lima-Barbero a,b, Sandra Díaz-Sanchez a, Olivier Sparagano c, Robert D. Finn d, José de la Fuente a,e and Margarita Villar a aSaBio.
    [Show full text]
  • Biogeochemical Insights Into Microbe–Mineral–Fluid Interactions in Hydrothermal Chimneys Using Enrichment Culture
    Extremophiles (2015) 19:597–617 DOI 10.1007/s00792-015-0742-5 ORIGINAL PAPER Biogeochemical insights into microbe–mineral–fluid interactions in hydrothermal chimneys using enrichment culture Nolwenn Callac1,2,3,4,8 · Olivier Rouxel5 · Françoise Lesongeur1,2,3 · Céline Liorzou4 · Claire Bollinger6 · Patricia Pignet1,2,3 · Sandrine Chéron5 · Yves Fouquet5 · Céline Rommevaux‑Jestin7 · Anne Godfroy1,2,3 Received: 12 December 2014 / Accepted: 1 March 2015 / Published online: 17 March 2015 © Springer Japan 2015 Abstract Active hydrothermal chimneys host diverse and electron donors between sulfate and iron reducers at microbial communities exhibiting various metabolisms high temperature. This approach allowed the cultivation of including those involved in various biogeochemical cycles. microbial populations that were under-represented in the To investigate microbe–mineral–fluid interactions in hydro- initial environmental sample. The microbial communities thermal chimney and the driver of microbial diversity, are heterogeneously distributed within the gas-lift bioreac- a cultural approach using a gas-lift bioreactor was cho- tor; it is unlikely that bulk mineralogy or fluid chemistry sen. An enrichment culture was performed using crushed is the drivers of microbial community structure. Instead, active chimney sample as inoculum and diluted hydro- we propose that micro-environmental niche characteristics, thermal fluid from the same vent as culture medium. Daily created by the interaction between the mineral grains and sampling provided time-series access to active microbial the fluid chemistry, are the main drivers of microbial diver- diversity and medium composition. Active archaeal and sity in natural systems. bacterial communities consisted mainly of sulfur, sulfate and iron reducers and hydrogen oxidizers with the detec- Keywords Active microbial diversity · Continuous tion of Thermococcus, Archaeoglobus, Geoglobus, Sul- enrichment culture · Deep-sea hydrothermal vent · furimonas and Thermotoga sequences.
    [Show full text]
  • A New Ciboria Sp. for Soil Mycoremediation and the Bacterial Contribution to the Depletion of Total Petroleum Hydrocarbons
    fmicb-12-647373 June 8, 2021 Time: 13:32 # 1 ORIGINAL RESEARCH published: 08 June 2021 doi: 10.3389/fmicb.2021.647373 A New Ciboria sp. for Soil Mycoremediation and the Bacterial Contribution to the Depletion of Total Petroleum Hydrocarbons Simone Becarelli1,2†, Ilaria Chicca1,3†, Salvatore La China4, Giovanna Siracusa1, Alessandra Bardi5, Maria Gullo4, Giulio Petroni1, David Bernard Levin2,3 and Simona Di Gregorio1* 1 Department of Biology, University of Pisa, Pisa, Italy, 2 BD Biodigressioni, Pisa, Italy, 3 Department of Biosystem Engineering, University of Manitoba, Winnipeg, MB, Canada, 4 Department of Life Sciences, University of Modena and Reggio-Emilia, Reggio Emilia, Italy, 5 Department of Civil and Environmental Engineering, University of Florence, Florence, Italy Edited by: A Ciboria sp. strain (Phylum Ascomycota) was isolated from hydrocarbon-polluted Sanket J. Joshi, soil of an abandoned oil refinery in Italy. The strain was able to utilize diesel Sultan Qaboos University, Oman oil as a sole carbon source for growth. Laboratory-scale experiments were Reviewed by: Muhammad Arslan, designed to evaluate the use of this fungal strain for treatment of the polluted University of Alberta, Canada soil. The concentration of total petroleum hydrocarbons (TPH) in the soil was Małgorzata Pawlik, University of Silesia in Katowice, 8,538 mg/kg. Mesocosms containing the contaminated soil were inoculated with Poland the fungal strain at 1 or 7%, on a fresh weight base ratio. After 90 days Enrique Eymar, of incubation, the depletion of TPH contamination was of 78% with the 1% Universidad Autónoma de Madrid, Spain inoculant, and 99% with the 7% inoculant.
    [Show full text]
  • Prevotella Jejuni Sp. Nov., Isolated from the Small Intestine of a Child with Coeliac Disease
    International Journal of Systematic and Evolutionary Microbiology (2013), 63, 4218–4223 DOI 10.1099/ijs.0.052647-0 Prevotella jejuni sp. nov., isolated from the small intestine of a child with coeliac disease Maria E. Hedberg,1 Anne Israelsson,1 Edward R. B. Moore,2,3 Liselott Svensson-Stadler,2 Sun Nyunt Wai,4 Grzegorz Pietz,1 Olof Sandstro¨m,5 Olle Hernell,5 Marie-Louise Hammarstro¨m1 and Sten Hammarstro¨m1 Correspondence 1Department of Clinical Microbiology, Immunology, Umea˚ University, SE-90187 Umea˚, Sweden Maria E. Hedberg 2CCUG – Culture Collection University of Gothenburg, Department of Clinical Bacteriology, [email protected] Sahlgrenska University Hospital, SE-41345 Go¨teborg, Sweden Sten Hammarstro¨m 3 [email protected] Department of Infectious Diseases, Sahlgrenska Academy of the University of Gothenburg, SE-40530 Go¨teborg, Sweden 4Department of Molecular Biology, Umea˚ University, SE-90187 Umea˚, Sweden 5Department of Clinical Sciences, Pediatrics, Umea˚ University, SE-90187 Umea˚, Sweden Five obligately anaerobic, Gram-stain-negative, saccharolytic and proteolytic, non-spore-forming bacilli (strains CD3 : 27, CD3 : 28T, CD3 : 33, CD3 : 32 and CD3 : 34) are described. All five strains were isolated from the small intestine of a female child with coeliac disease. Cells of the five strains were short rods or coccoid cells with longer filamentous forms seen sporadically. The organisms produced acetic acid and succinic acid as major metabolic end products. Phylogenetic analysis based on comparative 16S rRNA gene sequence analysis revealed close relationships between CD3 : 27, CD3 : 28T and CD3 : 33, between CD3 : 32 and Prevotella histicola CCUG 55407T, and between CD3 : 34 and Prevotella melaninogenica CCUG 4944BT.
    [Show full text]
  • Sponges on the South‑East Coast of India Ramu Meenatchi1, Pownraj Brindangnanam1,2, Saqib Hassan1, Kumarasamy Rathna1, G
    www.nature.com/scientificreports OPEN Diversity of a bacterial community associated with Cliona lobata Hancock and Gelliodes pumila (Lendenfeld, 1887) sponges on the South‑East coast of India Ramu Meenatchi1, Pownraj Brindangnanam1,2, Saqib Hassan1, Kumarasamy Rathna1, G. Seghal Kiran3 & Joseph Selvin1* Marine sponges are sources of various bioactive metabolites, including several anticancer drugs, produced mainly by sponge-associated microbes. Palk Bay, on the south-east coast of India, is an understudied, highly disturbed reef environment exposed to various anthropogenic and climatic stresses. In recent years, Palk Bay sufered from pollution due to the dumping of untreated domestic sewage, efuents from coastal aquaculture, tourism, salt pans, cultivation of exotic seaweeds, and geogenic heavy-metal pollution, especially arsenic, mercury, cadmium, and lead. Low microbial- abundant sponge species, such as Gelliodes pumila and Cliona lobata, were found to be ubiquitously present in this reef environment. Triplicate samples of each of these sponge species were subjected to Illumina MiSeq sequencing using V3–V4 region-specifc primers. In both C. lobata and G. pumila, there was an overwhelming dominance (98 and 99%) of phylum Candidatus Saccharibacteria and Proteobacteria, respectively. The overall number of operational taxonomic units (OTUs) was 68 (40 and 13 OTUs unique to G. pumila and C. lobata, respectively; 15 shared OTUs). Alphaproteobacteria was the most abundant class in both the sponge species. Unclassifed species of phylum Candidatus Saccharibacteria from C. lobata and Chelotivorans composti from G. pumila were the most abundant bacterial species. The predominance of Alphaproteobacteria also revealed the occurrence of various xenobiotic-degrading, surfactant-producing bacterial genera in both the sponge species, indirectly indicating the possible polluted reef status of Palk Bay.
    [Show full text]
  • Parvibaculum Lavamentivorans Gen. Nov., Sp. Nov., a Novel Heterotroph That Initiates Catabolism of Linear Alkylbenzenesulfonate
    Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate David Schleheck,1 Brian J. Tindall,2 Ramo´n Rossello´-Mora3 and Alasdair M. Cook1 Correspondence 1Fachbereich Biologie der Universita¨t, D-78457 Konstanz, Germany Alasdair M. Cook 2DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, D-38124 [email protected] Braunschweig, Germany 3CSIC–UIB–Institut Mediterrani d’Estudis Avanc¸ats, E-07190 Esporles, Mallorca, Spain Strain DS-1T is a small (0?8 mm in length and 0?2 mm in diameter) heterotrophic bacterium able to v-oxygenate the commercial surfactant linear alkylbenzenesulfonate (LAS) and shorten the side chain by b-oxidation to yield sulfophenylcarboxylates. The morphotype is widespread in cultures able to utilize LAS, and a second organism with similar characteristics, strain AN-8, is now available. Utilization of LAS is concomitant with formation of a biofilm, and cells were non-motile. Many surfactants were utilized. The organisms also grew with acetate or octane, but required no biofilm and were motile. Analysis of the gene encoding 16S rRNA placed the organisms in the a-subclass of the Proteobacteria with a sequence divergence of >8 % from any species whose name has been validly published. 16S rRNA gene sequence comparison with entries in the GenBank database showed 98 % similarity to an a-protobacterial marine isolate, JP57: strain JP57 displayed the same morphotype as strain DS-1T, but it was unable to utilize surfactants or any single source of carbon tested. The lipid components of strains DS-1T and JP57 were virtually identical. The fatty acids contained ester- and putative amide-linked hydroxy fatty acids, in a combination that is currently unique in the a-Proteobacteria.
    [Show full text]
  • Gravity-Driven Microfiltration Pretreatment for Reverse
    Desalination 418 (2017) 1–8 Contents lists available at ScienceDirect Desalination journal homepage: www.elsevier.com/locate/desal Gravity-driven microfiltration pretreatment for reverse osmosis (RO) MARK seawater desalination: Microbial community characterization and RO performance ⁎ Bing Wua, , Stanislaus Raditya Suwarnoa, Hwee Sin Tana, Lan Hee Kima, Florian Hochstrasserb, ⁎ Tzyy Haur Chonga,c, , Michael Burkhardtb, Wouter Pronkd, Anthony G. Fanea a Singapore Membrane Technology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One #06-08, 637141, Singapore b UMTEC, University of Applied Sciences Rapperswil, Oberseestrasse 10, 8640, Switzerland c School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore d EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, Duebendorf, CH -8600, Switzerland ARTICLE INFO ABSTRACT Keywords: A pilot gravity-driven microfiltration (GDM) reactor was operated on-site for over 250 days to pretreat seawater Assimilable organic carbon for reverse osmosis (RO) desalination. The microbial community analysis indicated that the dominant species in Biofouling the pilot GDM system (~18.6 L/m2 h) were completely different from those in the other tested GDM systems Eukaryotic community (~2.7–17.2 L/m2 h), operating on the same feed. This was possibly due to the differences in available space for Gravity-driven microfiltration eukaryotic movement, hydraulic retention time (i.e., different organic loadings) or operation time (250 days vs. Prokaryotic community 25–45 days). Stichotrichia, Copepoda, and Pterygota were predominant eukaryotes at genus level in the pilot GDM. Seawater pretreatment Furthermore, the GDM pretreatment led to a significantly lower RO fouling potential in comparison to the ultrafiltration (UF) system.
    [Show full text]
  • Shifting the Genomic Gold Standard for the Prokaryotic Species Definition
    Shifting the genomic gold standard for the prokaryotic species definition Michael Richter and Ramon Rossello´ -Mo´ ra1 Marine Microbiology Group, Institut Mediterrani d’Estudis Avanc¸ats (CSIC-UIB), E-07190 Esporles, Spain Edited by James M. Tiedje, Center for Microbial Ecology, East Lansing, MI, and approved September 16, 2009 (received for review June 11, 2009) DNA-DNA hybridization (DDH) has been used for nearly 50 years as of diversity among prokaryotes, the circumscription of each geno- the gold standard for prokaryotic species circumscriptions at the species would, in addition, be dependent on each group being genomic level. It has been the only taxonomic method that offered studied (2, 6). Nevertheless, the use of DDH has mainly driven the a numerical and relatively stable species boundary, and its use has construction of the current prokaryotic taxonomy, as it has become had a paramount influence on how the current classification has the gold standard for genomically circumscribing species. This been constructed. However, now, in the era of genomics, DDH parameter has had a similar impact in prokaryotic taxonomy as the appears to be an outdated method for classification that needs to interbreeding premise that is the basis for the biological species be substituted. The average nucleotide identity (ANI) between two concept for animal and plant taxonomies (1). In the late 1980’s (5), genomes seems the most promising method since it mirrors DDH taxonomists already believed that the reference standard for de- closely. Here we examine the work package JSpecies as a user- termining taxonomy would be full genome sequences. friendly, biologist-oriented interface to calculate ANI and the Despite being a traditional method, DDH has been often criti- correlation of the tetranucleotide signatures between pairwise cized as being inappropriate to circumscribe prokaryotic taxa genomic comparisons.
    [Show full text]
  • Plant and Bacterial Metaxin-Like Proteins: Novel Proteins Related to Vertebrate Metaxins Involved in Uptake of Nascent Proteins Into Mitochondria
    bioRxiv preprint doi: https://doi.org/10.1101/2020.03.02.972976; this version posted March 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Plant and Bacterial Metaxin-like Proteins: Novel Proteins Related to Vertebrate Metaxins Involved in Uptake of Nascent Proteins into Mitochondria Kenneth W. Adolph Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 Email Address: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.03.02.972976; this version posted March 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ABSTRACT The metaxins were originally identified as vertebrate proteins of the outer mitochondrial membrane involved in protein import into mitochondria. Metaxin proteins have also been found in diverse invertebrate phyla. The present study is concerned with examining whether metaxin- like proteins occur in plants and bacteria. Metaxin-like proteins were revealed by their homology with human metaxins and the possession of characteristic GST_Metaxin protein domains. The results demonstrate that metaxin-like proteins exist in plants that include a wide variety of angiosperms, both eudicots and monocots, and other plant groups. Metaxin-like proteins can also be detected in bacteria, particularly in the Proteobacteria phylum, but also in different bacterial phyla. Phylogenetic analysis indicates that plant metaxin-like proteins, bacterial metaxin-like proteins, and vertebrate metaxins form distinct phylogenetic groups, but are related. Metaxin-like proteins, however, are only distantly related to GSTs (glutathione S-transferase proteins).
    [Show full text]